Problem is that the GBU-39 can only penetrate about six feet of concreate, the only weapon that could take out a facility built under a mountain would be a nuke. More likely scenario would be some type of ground units going into the facility and using explosives to destroy it from the inside.
All tunnels have openings to the surface. Enough said.
What if they put through the front door, nice big thermobaric munition.